


AUGMENT

by startrekfan



Category: Star Trek: Alternate Original Series (Movies)
Genre: Adventure, Drama, Gen, fan fiction
Language: English
Status: In-Progress
Published: 2016-06-01
Updated: 2016-06-01
Packaged: 2018-07-11 16:33:05
Rating: Teen And Up Audiences
Warnings: Graphic Depictions Of Violence
Chapters: 5
Words: 4,535
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/7060507
Author URL: https://archiveofourown.org/users/startrekfan/pseuds/startrekfan
Summary: <blockquote class="userstuff">
              <p>After the events of Star Trek Into Darkness, Jim Kirk decided to investigate the secret and terrible "Section 31" after not being satisfied with the outcoming of what happened to Khan Noonien Singh, that was never taken to trial as expected, "disappearing" from any official record instead.<br/>He will join forcer with Carol Marcus and Scotty in order to find out more about the Section 31 and finally, try to expose it to the world, doing his best to take it down in the process.</p><p>The story will also explore Khan's side of story of his experiences during the one year he had to work under Marcus' control.<br/>Kirk and Khan are the main characters.<br/>There might be original characters.</p>
            </blockquote>





	1. REBEL

Some time had passed since the battle in space against Admiral Marcus and the crash of the Vengeance in San Francisco.  
Everything seemed to have calmed down after a while, the order seemed rigid, the system seemed to be working, everyone seemed satisfied, except for one person.

Jim Kirk had been thinking about the previous events, which had happened in such a wild, sudden way. The sudden turn of the facts by Alexander Marcus, who had revealed his true face, the mysterious super soldier, Carol Marcus and the mysterious “Section 31” plus the Vengeance, such powerful spaceship in secret, behind Jupiter.  
Things weren't the way Kirk wanted. It was all a façade, a fake peace, superficial appearances.  
What had happened to Khan after all those events?  
Everything pointed out to a simple direction, the hadn't been judged for his crimes how Jim wanted him to. So where was he now? Dead? Hard to believe.  
If there was something Kirk knew, it was that wrong things were still happening, terrible choices still being made and he couldn't simply do nothing about it.

He had been thinking while sitting on his bed.  
What could he do? He was just a man, could he change a reality alone?  
Even after all kinds of doubts crossed his mind, he finally came to a definitive conclusion.  
His hands firm over his own knees as he was sitting on the bed, he said out loud as if giving an order to himself.

“This is wrong.”  
The captain shook his head, his eyes fixed in the void.  
“There's gotta be a way to change this mess…”  
He narrowed his eyes.  
“There's gotta be.”

If Kirk had a power, it was all about his determination mixed with his ideals and impulses. Things were wrong and he would change them.  
That what he decided that morning.

He stood, sure of himself.  
He would find a way to change all the mistakes that currently were being hidden by the Union, by the Star Fleet, by his superiors.

“Carol, I really need to talk to you, listen...there is a café in…-look, I'll send the address. I'll need you to meet me there. As soon as you can. Even if you're busy, I don't know, just...just go there as soon as you can.”

That was the message he sent Carol Marcus, the woman who could be the key to the situation.  
She knew about the Vengeance, she knew about the Section 31 and she was Alexander Marcus' daughter. She knew. She had to know. Kirk thought and kept saying that to himself.  
The so energetic man wore a dark jacket and dashed to said café, waiting for Carol, so anxious, it had to be now, he had to go there, even if he had to wait the whole day for Carol, he couldn't simply sit and wait.

That was Jim Kirk.


	2. DATA

Gladly for Kirk, Carol didn't take long to get there. Kirk impatiently waited while sitting, both his elbows on the table, his hands touching his head, thinking of how his movements would be.  
Everything was a big gut feeling, but he knew he had to think.  
It was still morning, it was raining slightly over the city, when Carol finally saw the captain and sat in front of him.

“I'm so glad you came.”  
Kirk said, as if confessing the storm that was happening inside him.  
Carol leaned slightly closer, already knowing she hadn't gone there just to have a coffee. She knew it was serious, it had been clear from Kirk's tone of voice in the audio message he had sent her.  
She leaned slightly forward, her face serious, focused.  
“What happened?”  
The young woman asked, her eyes already showing she was determined to help.

The captain took a deep breath before talking. Now that she was there, ready to listen to him, he was even more motivated to follow his will.

They were sitting in a retro style coffee shop, in one of the most private areas of the place, where he knew no one would overhear them, specially their conversation just seeming to be friends talking about ordinary things.  
He finally spoke.  
“Khan. What the hell happened to him after everything that happened?”  
Carol's eyes looked away the moment Jim mentioned the name. She knew.  
She moved her eyes back to Kirk, trusting that if he wanted to know such a thing in a such serious way, it was because he had a great cause behind his actions.  
“He was put inside a cryogenic tube and was joined with his crew. They're all in...in what you may say that was left from the Section 31.”  
Kirk's eyes narrowed slightly.  
“Was he judged?”  
Carol shook her head and closed her eyes.  
“No.”  
The captain now was sure of his gut feeling, justice wasn't being made. But not justice for itself, justice for what was right wasn't being made.  
“What are they going to do to him?”  
The admiral's daughter face seemed even more serious, she let out a sigh, showing how tense the situation was.  
“They are already doing things to him.”  
Silence.  
She continued.  
“Things seem to have changed into worse. After my father's death, the superiors made sure to bury the Section31's secrets even more, and to make things worse, there is not a definitive person controlling the course of the actions, but a team. A team of men and women that know what they are doing, that know all the dark secrets from that section and that have decided to keep them secret.  
The authority they have...the power in their hands...it became impossible even for me to gain access to certain things as I used to have.”  
Jim gave her a slight nod, as if showing he understood how grave the whole situation was.  
“I need a favor.”  
The man said.  
Carol didn't say a word, she just waited, she was listening and clearly willing to help.  
“I need to take a look in some files. I need to know what I can do to change things.”  
She shook her head.  
“It is not that easy...it is not that simple to just...change things. You'll need a plan...and information.”  
Kirk looked right into her eyes.  
“You know the information part? That's why I asked you to come here. What kind of access do you still have?”  
Carol responded determined.  
“I might not have direct access to the updated files of the Section 31...but I do have access to previous files. I can show you even from any computer screen, I learned how to make my access undetectable over time, if I try to search for old files, I'm sure they wouldn't notice and even if they did, they wouldn't know it was me. I can block certain...data.”  
She was an advanced weapons specialist, of course she had sharp computer code skills, which she had been using for some time now, since she was trying to find out about torpedoes when her father was still alive.  
The woman was decided.  
“We'll need a computer and an hotel room in an anonymous name so no one will be able to link the access directly to us, if we end up detected. Who else is coming?”  
Kirk let out a slight smirk.  
“Scotty.”


	3. TEAM

“What? But I am busy! Who do you think you are calling me in a day like this!?”  
Scotty said while holding the communicator in front of his face.  
“Listen, Scotty, we need your help, it...it is damn important, you better come, you have to come!”  
Kirk said, his voice in that strong determined tone.  
“Ahn...fine...but only because you said you NEED me, alright?”  
Jim's voice now sounded relieved.  
“Thank you Scotty.”  
The engineer's voice still seemed bothered as he spoke.  
“See if you give me a break you mad bastard…!”  
The captain just chuckled. That was Scotty.

“So?”  
Carol asked, already sitting facing Kirk, them both already in the hotel room, a short glass table between them, one chair still empty, where Scotty would be sitting in a few moments.  
Jim answered calmly, but still with such determination behind his words.  
“Scotty's coming. Very well, we can start. I'm decided to do this and it won't take long until he gets here.”  
She raised an eyebrow.  
“How can you be so sure?”  
The captain smiled.  
“This was his day off.”

Carol turned the portable computer she had brought and started to access the Star Fleet database. A few codes, passwords and another procedures and a an amount of folders appeared on the screen.  
Kirk frowned.  
“There they are...the so secret files about the so secret section….”  
He was unquiet inside, he wanted so much to simply solve everything out and end all of the wrong doing regarding those files, regarding that section.  
“What exactly did you want to know about.”  
Kirk was clear and objective.  
“I want to know about Khan. You said things were happening to him. Can you have access to them?”  
Carol sighed.  
“No. I can't have access to new information, but I can clarify you about what was done to him so far.”  
Jim leaned forward, observing the computer screen closer.  
“Bring it on.”  
She clicked on a specific folder and typed a password once again plus a few computer codes and satrted to speak.  
“Alright, we're in. I think that if you want to understand the situation as a whole...maybe we should first watch a few files about the Section 31 security cameras. I already watched these, it might be...well. You'll see for yourself.”  
Kirk seemed focused.  
“Okay. The first folder first.”  
She opened the file and a video started on screen.  
A video that would lead us...a bit more than one year to the past.


	4. CHAINS

Section 31, a certain day of a bit more than one year ago.  
An aggressive voice seems to be shouting.  
“HE STILL WON'T SPEAK? SHOCK THE HELL UP OF HIM AND LET ME ASK AGAIN!”  
Two men are holding a familiar figure, each man holding one arm, the figure's body as almost collapsing to the floor, tired, exausted.  
One of the agents said as if trying to calm the admiral who was shouting.  
“Sir...he still hadn't the time to fully recover from the cryogenic sleep...he still isn't...”  
The aggressive voice continued.  
“Make him speak!”  
The agent hesitated.  
“But Admiral Marcus...we might kill him if we…---”  
Marcus interrupted once again.  
“If he die all we have to do is to open another cryogenic tube, now shock him up!”  
The agents let go of the man they were holding, who fell at the same moment, spread on the floor.  
A specific pistol was drawn by one of the men, pointed to the one spead on the floor.  
The trigger was pressed, a metal wire was fired against the man on the floor's body, a visible wave of electricity crossed the wire, a loud pained shout came out from that familiar person.

Kirk frowned while watching that video.  
“That's...that's Khan...”

Khan started to shake on the floor as that heavy amount of electricity reached his body, now shaking, he turned, now his back facing the ground, the augment panting heavily.  
Marcus stood and walked closer to Khan's figure on the floor, but still keeping certain distance.  
“Did you hear what they said? They said you're recovering. But do you know what I think? I think you don't want to cooperate with me. What's your name? Uhnm? Are you still gonna be quiet?”  
The admiral signed to the agent holding the pistol, he pressed the trigger again, making the electricity once more Khan shouting in agonizing pain.  
He seemed and was weak indeed.  
Once the shock stopped, Marcus stepped over Khan's neck, looking to his tired face from above.  
“I asked about your name.”  
Khan had his eyes closed because of the pain, because of the weakness and the shock, but his spirit seemed strong as ever.  
He opened his deep brown eyes, rebel eyes.  
“Khan...is my name.”

Marcus didn't like the way Khan stared him. Even after staring back, Khan's eyes still were there, sharp like a sword.  
The admiral smirked.  
“I see we'll have to do a thing about these rebel eyes, don't we? Maybe you'll treat me with some more respect…?”  
He signed to the other agent, who crouched near Khan and pulled his head up by his hair.

Marcus went to his drawer and took a lighter, walking back to Khan slowly, as if even enjoying that moment of power over that creature, currently harmless because of the sudden shock of being removed from his cryotube without the correct procedures.  
The other agent made sure to hold Khan's both arms tight, the augment barely being able to keep his eyes open.  
Marcus then also crouched, smirking at the man in front of him, clearly unable to move an arm or leg, still with such rebel look.  
The admiral opened the lighter with his finger, a tiny source of flame now coming from it.  
“You know what? Screw you. I think I'll just get as much information I can from this one...and once you die I'll just take another human ice cream and do the same.”  
Khan's eyes widened in fear. His mind was still so lost, his memories so confused from the sudden awaking from the long sleep in such a violent way.  
The admiral smirked more.  
“I see you're starting to understand what is going on here. I have quite a bunch of frozen men like you. I can do anything I want to them, just like I can do anything to you. Now give me your right eye here.”  
The agent made sure to keep Khan's eye open, Marcus slowly approaching the lighter's flame close to his eye.  
The cruel man spoke once more.  
“After this...I'm sure you will cooperate. But not it is personal, you know? That look you gave me...no one ever dared to stare me like that before.”  
The admiral had experienced fear that moment.  
“And now I'll show you who in charge here.”  
Marcus pressed the lighter against Khan's eye, a loud savage shout taking over the room.

Carol watching the video with Kirk just closed her eyes. Kirk himself had his own open wide in terror. Khan, that man, that structure, that fortress who seemed invincible so vulnerable spread on the floor, unable to react, unable to fight back, being tortured like a beast in Marcus' hands.

The shouts continued for the next ten minutes, the agents shocking Khan whenever he was about to faint, keeping him awake.  
After Marcus pulled the lighter away, the augment on the floor could only pant in despair, he barely could breath, his whole body aching, his right eye now completely ruined, the pain taking over his whole head.  
Marcus sighed.  
“See how it is? I can do this to every single one of those frozen shits like you. Do you want me to do so?”  
The admiral stopped speaking when he saw Khan's left eye. The look coming from it wasn't staring so sharply like before, but even so, there seemed to be an huge strength coming from it, Alexander Marcus still felt fear, a fear he was doing his best to hide.  
“Alright, now you pissed me off. You two, drag him to that room.”  
The two men obeyed.  
Inside the specified room there were three cryogenic tubes, but everything was dark, nothing was clear.  
Marcus reached the room and turned the light on.  
Once he did, Khan's heart skipped a beat, his chin fell on despair, he even failed to shout.  
Right in front of him there was an opened cryogenic tube, the fellow augment inside had both his eyes opened wide, he was dead, motionless.  
Khan's left eyes became wet, tears of despair started to roll down, the pain of his ruined right eye seemed nothing compared to what his heart was feeling. He couldn't stopped fixing that corpse, one member of his crew, one member of his family, one of those he loved the most.  
Marcus just observed the augment's reaction.  
“I had asked your name.”  
The secretly cruel man asked.  
Khan was still in shock, fixing his friend, dead, inside that opened tube.  
Marcus gritted his teeth and kicked Khan's face hard, stepping back right after it.  
A scared, desperate voice came out from the augment's mouth, his hair all over his face, blood dripping from the right side of his face to the floor, tears dripping from the left.  
“Khan Noonien Singh...Khan Noonien Singh is my name!”  
The admiral smirked ironically.  
“Now we're helping, eh? Look at the mess you're making me do.”  
He shook his head.  
“You're Khan Noonien Singh...uhn? Right. I want you to give me information.”  
Noonien was quiet, barely breathing, scared, his stomach shaking in terror, tense, his muscles still weak, because of the cryogenic awakening, because of the pain, because of the sadness.  
The admiral signed for one of the two agents, who let go of Khan's hair and pulled another cryogenic tube nearby. It was closed.  
The metal structure made a loud tormenting noise as it was dragged closer, Khan's heart racing.  
Alexander Marcus was objective with his word.  
“Open it up.”  
He ordered he agent.  
Khan panicked.  
“No…wait! If you simply open it without the procedure the..--”  
The admiral kicked his face again, stronger than last time, more of the augment's blood spreading over the floor.  
Khan couched as he tried to recover from that violent impact.  
Alexander showed what his other hand was holding. A pistol.  
“Do you know what this is…?”  
Noonien had his eye fixed on Marcus, so scared.  
The cruel admiral continued.  
“This is a pistol...a shot from this beauty...and you're dead.”  
Khan's eye moved to the cryogenic tube, the agent was tryint to pull it open.  
The augment start to shook his head as if meaning “no”.  
As the agent was pulling the tube open, a metallic noise was coming out.  
“NO! DON'T!!”  
He shouted as his voice was shaking so much, only to be interrupted by Marcus' kick once again.  
“Look at me when I'm talking to you!”  
Alexander stepped closer to the tube.  
Khan quiet, his eye wide following the man's movements.  
Finally, a louder noise came out, the agent had pulled the tube open, all at once.  
A shout started to form inside Khan, but before it could come out, a sequence of loud noises silenced him, Marcus had just fired whoever was inside that cryogenic tube several times.  
Four seconds of shock and silence and then Khan started to shout, out of control, a shout of terror, trying to react, trying to stand, still so weak, the agent holding his arms containing his movements.  
The electric gun's trigger was pressed again, another strong wave of electricity attacked Khan's body, making the shouts sound even more desperate.  
After the terrifying noises, silence once more.  
Noonien Singh was quiet on the floor, shaking slightly because of the damage, small sobs could be heard coming from him, the man was crying, lost in despair.  
Slowly, he started trying to move again, weakly.  
The admiral signed the agent to let go of the augment.  
Khan slowly dragged himself close to the now dead companion. Once he was close, he cupped his friend's cold face with both his hands, the corpse clearly wounded from Marcus' shots, lifeless.  
The moaning coming from Khan's lips became louder, he could do nothing, it was clear those he loved were in Marcus' hands, there was nothing he could do against that man.

Soon one of the agents pulled Khan back to the middle of the room, Marcus crouched near him again.  
“Did you get it now…? Did you get it…? Do you want me to open another tube?”  
Khan was quick to answer.  
“NO!”  
Alexander pulled Khan's hair.  
“I didn't hear it.”  
Noonien closed his eyes tight and repeated.  
“NO SIR!”  
The admiral's lips smirked.  
“Now it is a lot better. Hey you.”  
He pointed to the third still closed cryogenic tube.  
“Open it up?”  
Khan started to panic again.  
“No...NO! I'LL DO WHATEVER YOU WANT! PLEASE DON'T! I BEG YOU!”  
The other tube was opened violently again, Khan already started to shout, Marcus letting go of him and stepping behind.  
The agent nodded to the sign Marcus had given him and once the tube was opened, he started to shot the woman who was in deep cryogenic sleep inside.  
The augment's shout became another desperate cry, slowly he let his body fall against the floor again, weeping, living that nightmare that was so real.  
Once the augment went quiet again, Marcus approached again, the two men grabbing and holding Khan's arms to make sure he wouldn't react, Noonien still so weak.  
Marcus started to speak yet again.  
“I will so this each time you commit a mistake. Each time you lie. Each time you look me in a way I don't you to look me, do you understand?”  
Khan didn't move, his eyes so tired, so in shock, his lips finally answering, doing its best so those he loved wouldn't be sacrificed.  
“Yes...sir...I…understand.”  
Noonien was about to collapse.  
Alexander frowned and ordered.  
“I want you to stand. Now.”  
The agents let go of Khan, who slowly and pitifully tried to stand, his legs shaking, his right eyes aching, his heart so broken.  
After a few seconds, as ordered, the augment stood.  
Marcus stepped closer.  
“Very well. Now I want you to bow.”  
Khan obeyed, slowly moving his shaking knee, he bowed.  
The admiral seemed satisfied.  
“Good.”  
He threw his lighter to one of the agents.  
“Now this...is because of that look you gave me.”  
Marcus spoke, so much hate in his voice.  
“You there, burn his other eye.”  
The admiral left the room, slamming the door, the video ending as more shouts would take over all the room.


	5. SOUL

Kirk's eyes were filled with horror as he watched those video tapes, it was so disturbing.  
He was speechless.  
Carol noticed how the captain seemed bothered because of what he had just seen, but remained quiet, waiting for Kirk's reaction.  
The man shook his head, putting his hands together as if thinking deeply.  
"I never imagined Khan had gone through so much..."  
She sighed.  
"This was only the beginning. Khan's eyes recovered eventually and he was put to develop new weapons while under constant menace. Once he learned how to deal with the actual days technology, he started tampering with the cameras in a way he could try to find his own ways of how to escape and rescue his crew...but in the end everything failed and well, you know what happened. The attack against Section 31...the attack during the meeting...he being a prisoner in the Enterprise..."

Kirk's eyes seemed lost, deep in thought.  
"He probably thinks his crew is dead..."  
Carol only nodded.  
"Yes, with all I know so far, he wasn't informed his crew was safe. All I know is that...during that year he was being treated like a slave by my father...he never gave up hope. Not even for a moment. It was possible to see determination in his eyes.  
You know, sometimes I happened to see him and even interact with him professionally, like when the sector he was working on needed my skills with advanced weapons, things like that."  
The captain finally moved his eyes, looking to Carol.  
"And...how did he behave? Khan was just like when we talked to him in the Enterprise or...?"  
She let out a sigh.  
"Well, not completely. He normally was very objective and serious, he never mentioned or talked about anything unrelated to his work. There were times he was acting coldly as usual, there were times he just seemed so sick and weak, but even so he worked the harder he could. I never saw such a thing..."  
She seemed to be remembering clearly the events of that year.  
"You never saw such a thing what...?"  
Kirk asked, objectively, serious, worried.  
Carol moved her eyes to Jim.  
"I don't know...he was...always so serious with everything he was doing. Whenever he started a project he would lead it and work on it until it reached perfection...  
At first I thought that was natural from his personality...you know, probably it is a bit, but then I began to notice how he was pushing himself in a very uncommon manner...it was then that I started to think something was out of place...  
There were strange...things happening, files disappearing...projects without specified details...I imagined there was something wrong...as if my father was hiding specific things.  
Sometimes I would just...cross paths with Khan and...like I said, there were times he looked so ill...so...so outworn..."

Jim raised his eyebrows.  
"He went through a lot of...things...just...just how things can be so worse than I expected them to be...? Clearly your father was using Khan to develop those weapons, just like he had mentioned, like that huge dark ship and that portable transwarp beaming device..."  
Khan probably used that to escape from the Section 31 during gaps so he could set up his plan to escape..."  
Carol gave Kirk a nod.  
"Yes, the portable transwarp beaming device was one of the first projects he worked on. It was basically just him...all the others would just work on some details and tests. My father was angry because he didn't know exactly what that project was...it was then that Khan started working in many projects at the same time, and it was then that he began to look so tired. Probably he spent several nights without sleep.  
When I started investigating the projects my father was hiding...I found out about the Vengeance, I found out Khan was working on it...then later I found out about the torpedoes...but I had no idea Khan would have used them to hide his crew and try to smuggle them into safety. As soon and Khan tried to do so, my father obviously got scared about how all the secrets could be revealed if the torpedoes fell in the wrong hands...so he ordered you to fire the torpedoes...what would have killed Khan in Kronos...and erased almost every evidence of what my father was doing."

Kirk went quiet as Carol spoke, listening every word, imagining every detail. He could even see Khan trying to work with so many things at the same time, he could even see him being as cold as he could to not cause trouble.  
"He suffered hell in that Section 31...and now he is there again...  
We've gotta get him out of there. We've gotta."

As soon as Kirk finished his phrase, knocks on the door could be heard.  
"Ahn...hello there?"  
It was Scotty. It was obvious it was Scotty.  
Kirk stood and walked to open the door.


End file.
